Variant report

Variant	rs28910271
Chromosome Location	chr3:142269075-142269076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142267438..142270247-chr3:142280572..142282585,2	MCF-7	breast:
2	chr3:142262100..142263612-chr3:142267272..142269416,2	K562	blood:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs28897764	1.00[GIH][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28897765	0.87[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28910270	0.83[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28910272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34104088	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34213965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34383865	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34678750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34686786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35264204	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35363608	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35404216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35440390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35988759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35993426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36090479	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7618253	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28910271	PLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
3	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
5	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
6	chr3:142209400-142271800	Weak transcription	HepG2	liver
7	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
8	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
9	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
11	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
12	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:142242400-142275800	Weak transcription	NHEK	skin
15	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
16	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:142251800-142270800	Weak transcription	Fetal Kidney	kidney
19	chr3:142251800-142271600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:142253200-142269600	Weak transcription	Pancreas	Pancrea
21	chr3:142253200-142271200	Weak transcription	Psoas Muscle	Psoas
22	chr3:142253200-142271800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:142253400-142270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:142253400-142270600	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:142253400-142270800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:142253600-142271600	Weak transcription	Brain Angular Gyrus	brain
29	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:142254000-142270000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:142255600-142269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:142255600-142270000	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:142255600-142270000	Weak transcription	Placenta	Placenta
34	chr3:142255600-142270600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:142255600-142270800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:142255600-142271400	Weak transcription	Ovary	ovary
37	chr3:142255600-142273800	Weak transcription	Gastric	stomach
38	chr3:142255600-142274200	Weak transcription	NHLF	lung
39	chr3:142255800-142270600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:142256200-142283600	Weak transcription	Aorta	Aorta
41	chr3:142257200-142274200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:142259400-142270000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:142259800-142269400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:142259800-142285600	Strong transcription	Dnd41	blood
45	chr3:142262400-142271000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:142262400-142271800	Weak transcription	Osteobl	bone
47	chr3:142263000-142270600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:142263200-142269800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:142263200-142273800	Strong transcription	Monocytes-CD14+_RO01746	blood

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